4.2.1-1 Release Notes

Two new beta tools have been released: fq2bamfast and minimap2.

A new beta pipeline has been released: pacbio_germline.

Performance improvements include fq2bamfast, a faster version of the existing fq2bam and the ability to run the variant caller in germline and deepvariant_germline in parallel with BAM generation.

A number of bugs have been fixed. Most notably, fq2bam read filtering could have failed with read sizes more than ~500 basepairs.

New Tools

With this release we have added two new tools:

• fq2bamfast
• minimap2

We have also added one new pipeline:

• pacbio_germline

The new beta fq2bamfast is a re-implementation of accelerated BWA-MEM present in fq2bam to better utilize GPUs such as A100 and H100.

Improvements

Tool Updates

mutectcaller:

• Adds the following new options:

  • --active-probability-threshold
  • --genotype-germline-sites
  • --genotype-pon-sites
  • --initial-tumor-lod
  • --mutect-bam-output
  • --pruning-lod-threshold
  • --tumor-lod-to-emit
  • -max-reads-per-alignment-start (as part of the --mutectcaller-options option)

fq2bam and associated pipelines: germline pipeline, deepvariant_pipeline, and somatic pipeline:

• New compression options for --gpuwrite: use --gpuwrite-deflate-algo 3 for more compression at slightly slower speed and --gpuwrite-deflate-algo 0 for more speed, which continues to be the default.
• Fix edge case with FASTQ filtering.

Improvements Spanning Multiple Tools

• Added the --read-from-tmp-dir option to germline pipeline and deepvariant_pipeline. It will run the variant caller in parallel with BAM generation. It has been tested on A100 and H100 but might cause out-of-memory on other GPUs.
• Added the --fq2bamfast option to germline pipeline, deepvariant_pipeline, and somatic pipeline to use fq2bamfast for alignment.

For further information refer to the Parabricks datasheet.